Major supply and transport routes to parts of Australia's tropical north were cut Wednesday after wild weather derailed a freight train and destroyed sections of a major highway.

Storms linked to ex-tropical cyclone Grant caused flash flooding across the remote Northern Territory that washed a 33-wagon iron ore train off a bridge and swept slabs of roadway from the Stuart Highway.

The Territory's chief minister Paul Henderson said there had been "significant damage" to roads and engineers were yet to inspect bridges.

"Until the waters recede we're not going to have a clear picture as to the structural impacts ... so we're hoping that the waters recede as quickly as they came up," Henderson told ABC Radio.

The damage means that access to the Territory's tropical north, known locally as the Top End, is reliant on air travel, prompting concern about restocking supermarkets and other essentials.

"We have got an issue now with supplies," said Willem Westra Van Holthe, a local politician from the town of Katherine, which gets most of its food from Darwin, further north.

"Shelves will be hit pretty hard, I would imagine."

Henderson said he was hopeful of reopening the arterial Stuart Highway within 48 hours but the rail link was likely to take longer.

The derailed freight train's operators Genesee and Wyoming said crews were inspecting the damaged 350-metre (1,150 foot) segment and "it is not yet known how long repairs will take."

Genesee and Wyoming said an empty crew van and five wagons -- two of which contained hazardous copper concentrate -- were derailed when flood waters washed away the southern base of the Edith River bridge north of Katherine.

Copper concentrate is considered a hazardous substance and inspectors from the environment department are investigating whether there has been any leak.

"We're taking it pretty seriously," a department spokeswoman said.

The railway damage has left The Ghan passenger train, which runs through Australia's desert Outback from the southern city of Adelaide to Darwin, stranded in Katherine with about 200 passengers on board.

"The Stuart Highway is also presently closed north of Katherine and we have now been advised it will be closed for an estimated time of 48 hours," said operator Great Southern Rail.

Grant was downgraded to a tropical low on Monday but it is expected to return to cyclone strength on Friday as it crosses the Gulf of Carpentaria to neighbouring Queensland state.